Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account

The emergence of a more transmissible variant of SARS-CoV-2 (B1. 1.7) in the United Kingdom (UK) during late 2020 has raised major public health concerns. Several mutations have been reported in the genome of the B.1.1.7 variant including the N501Y and 69-70deletion in the Spike region that has implications on virus transmissibility and diagnostics. Although the B.1.1.7 variant has been reported by several countries, only three cases have been reported in Pakistan through whole-genome sequencing. Therefore, the objective of the study was to investigate the circulation of B.1.1.7 variant of concern (VOC) in Pakistani population. We used a two-step strategy for the detection of B.1.1.7 with initial screening through TaqPathTM COVID-19 CE-IVD RT-PCR kit (ThermoFisher Scientific, Waltham, US) followed by partial spike (S) gene sequencing of a subset of samples having the spike gene target failure (SGTF). From January 01, 2021, to February 21, 2021, a total of 2,650 samples were tested for SARS-CoV-2 and 70.4% (n = 1,867) showed amplification of all the 3 genes (ORF, N, and S). Notably, 29.6% (n=783) samples have been SGTF that represented numbers from all the four provinces and suggest a rather low frequency during the first 3 weeks of January (n = 10, n = 13, and n = 1, respectively). However, the numbers have started to increase in the last week of January, 2021. During February, 726 (93%) cases of SGTF were reported with a peak (n = 345) found during the 3rd week. Based on the partial sequencing of SGTF samples 93.5% (n = 29/31) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. In conclusion, our findings showed an upsurge of B.1.1.7 cases in Pakistan during February, 2021 affecting 15 districts and warranting large scale genomic surveillance, strengthening of laboratory network and implementation of appropriate control measures in the country.

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An upsurge of SARS CoV-2 B.1.1.7 Variant in Pakistan

10.1101/2021.02.26.21252562 ◽

2021 ◽

Author(s):

Massab Umair ◽

Muhammad Salman ◽

Zaira Rehman ◽

Nazish Badar ◽

Abdul Ahad ◽

...

Keyword(s):

Large Scale ◽

Low Frequency ◽

Whole Genome ◽

Initial Screening ◽

Gene Target ◽

Health Concerns ◽

Partial Sequencing ◽

Spike Gene ◽

The United Kingdom ◽

High Prevalence

The emergence of a more transmissible variant of SARS-CoV-2 (B1.1.7) in the United Kingdom (UK) during late 2020 has raised major public health concerns. Several mutations have been reported in the genome of the B.1.1.7 variant including the N501Y and 69-70deletion in the Spike that has implications on virus transmissibility and diagnostics. Although the B.1.1.7 variant has been reported from several countries, only two cases have been identified through whole-genome sequencing from Pakistan. We used a two-step strategy for the detection of B.1.1.7 with initial screening through ThermoFisher TaqPathTM SARS-CoV-2 kit followed by partial sequencing of Spike (S) gene of samples having spike gene target failure (SGTF) on real-time PCR. From January 01, 2021, to February 21, 2021, a total of 2,650 samples were tested for the presence of SARS-CoV-2 using TaqPathTM kit and 70.4% (n=1,867) showed amplification of all the 3 genes (S, N, and ORF). Notably, 29.6% (n=783) samples had the spike gene target failure (SGTF). The SGTF cases were detected at a low frequency during the first three weeks of January (n=10, n=13, and n=1 respectively) however, the cases started to increase in the last week. During February, 726 (93%) cases of SGTF was reported with a peak (n=345) found during the 3rd week. Based on the partial sequencing of spike gene of SGTF samples (n=15), 93% (n=14) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. Our findings highlight the high prevalence of B.1.1.7 in Pakistan and warrant large scale genomic surveillance and strengthening of laboratory network in the country.

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Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

10.21203/rs.3.rs-551208/v1 ◽

2021 ◽

Author(s):

Zain Mushtaq ◽

Sadia Shakoor ◽

Akbar Kanji ◽

Najma Shaheen ◽

Asghar Nasir ◽

...

Keyword(s):

Binding Sites ◽

Rt Pcr ◽

Pcr Assay ◽

Gene Target ◽

Missed Opportunities ◽

Spike Gene ◽

Diagnostic Assays ◽

Additional Testing ◽

Pcr Assays ◽

Possible Cause

Abstract Objective: To investigate the possible cause of discrepancy between clinical and RT-PCR based diagnosis of patients with COVID-19.Results: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested using the Roche SARS-CoV-2 Cobas assay and were found to be negative. Further investigation for other viral causes of pneumonia was conducted using the Filmarray RP2.1 assay, which identified SARS-CoV-2 as the pathogen in all ten cases. To investigate whether this could be due to discrepancies between PCR assay, additional testing was conducted using the TaqPath TM COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, could be due to variation in the primer binding sites. The identification of strains with SGTF identify the possible presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.

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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

PLoS Biology ◽

10.1371/journal.pbio.3001236 ◽

2021 ◽

Vol 19 (5) ◽

pp. e3001236

Author(s):

Chantal B. F. Vogels ◽

Mallery I. Breban ◽

Isabel M. Ott ◽

Tara Alpert ◽

Mary E. Petrone ◽

...

Keyword(s):

South Africa ◽

United Kingdom ◽

Severe Acute Respiratory Syndrome ◽

Immune Responses ◽

Primary Target ◽

Pcr Assay ◽

Gene Target ◽

Spike Gene ◽

The United Kingdom ◽

The World

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (COVID-19) PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

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Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.10.2100130 ◽

2021 ◽

Vol 26 (10) ◽

Author(s):

Vítor Borges ◽

Carlos Sousa ◽

Luís Menezes ◽

António Maia Gonçalves ◽

Miguel Picão ◽

...

Keyword(s):

Confidence Interval ◽

Age Distribution ◽

Rt Pcr ◽

Gene Target ◽

Spike Gene ◽

Viral Loads ◽

Late Detection

We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83–95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.

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Increased hazard of death in community-tested cases of SARS-CoV-2 Variant of Concern 202012/01

10.1101/2021.02.01.21250959 ◽

2021 ◽

Cited By ~ 4

Author(s):

Nicholas G. Davies ◽

Christopher I. Jarvis ◽

W. John Edmunds ◽

Nicholas P. Jewell ◽

Karla Diaz-Ordaz ◽

...

Keyword(s):

Absolute Risk ◽

Care Home ◽

Pcr Amplification ◽

Deprivation Level ◽

Severe Illness ◽

Gene Target ◽

Spike Gene ◽

Risk Of Death ◽

The United Kingdom ◽

Novel Variant

VOC 202012/01, a SARS-CoV-2 variant first detected in the United Kingdom in September 2020, has spread to multiple countries worldwide. Several studies have established that this novel variant is more transmissible than preexisting variants, but have not identified whether it leads to any change in disease severity. We analyse a large database of SARS-CoV-2 community test results and COVID-19 deaths, representing 52% of all SARS-CoV-2 community tests in England from 1 September 2020 to 5 February 2021. This subset of SARS-CoV-2 tests can identify VOC 202012/01 because mutations in this lineage prevent PCR amplification of the spike gene target (S gene target failure, SGTF). We estimate that the hazard of death among SGTF cases is 58% (95% CI 40–79%) higher than among non-SGTF cases after adjustment for age, sex, ethnicity, deprivation level, care home residence, local authority of residence and test date. This corresponds to the absolute risk of death for a male aged 55–69 increasing from 0.6% to 0.9% (95% CI 0.8–1.0%) over the 28 days following a positive test in the community. Correcting for misclassification of SGTF and missingness in SGTF status, we estimate a 71% (48–97%) higher hazard of death associated with VOC 202012/01. Our analysis suggests that VOC 202012/01 is not only more transmissible than preexisting SARS-CoV-2 variants but may also cause more severe illness.

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Self-collection and pooling of samples as resources-saving strategies for RT-PCR-based SARS-CoV-2 surveillance, the example of travelers in French Polynesia

10.1101/2021.06.17.21254195 ◽

2021 ◽

Author(s):

Maite Aubry ◽

Iotefa Teiti ◽

Anita Teissier ◽

Vaea Richard ◽

Teheipuaura Mariteragi-Helle ◽

...

Keyword(s):

Large Scale ◽

Rna Extraction ◽

French Polynesia ◽

Rt Pcr ◽

Spike Gene ◽

First Case ◽

Main Challenge ◽

Positive Individual ◽

Human Material ◽

Specific Amplification

In French Polynesia, the first case of SARS–CoV–2 infection was detected on March 10th, 2020, in a resident returning from France. Between March 28th and July 14th, international air traffic was interrupted and local transmission of SARS–CoV–2 was brought under control, with only 62 cases recorded. The main challenge for reopening the air border without requiring travelers to quarantine on arrival was to limit the risk of re–introducing SARS–COV–2. Specific measures were implemented, including the obligation for all travelers to have a negative RT–PCR test for SARS–CoV–2 carried out within 3 days before departure, and to perform another RT–PCR testing 4 days after arrival. Because of limitation in available medical staff, travelers were provided a kit allowing self–collection of oral and nasal swabs. In addition to increase our testing capacity, self–collected samples from up to 10 travelers were pooled before RNA extraction and RT–PCR testing. When a pool tested positive, RNA extraction and RT–PCR were performed on each individual sample. We report here the results of COVID–19 surveillance (COV–CHECK PORINETIA) conducted between July 15th, 2020, and February 15th, 2021, in travelers using self–collection and pooling approaches. We tested 5,982 pools comprising 59,490 individual samples, and detected 273 (0.46%) travelers positive for SARS–CoV–2. A mean difference of 1.17 Ct (CI 95% 0.93 – 1.41) was found between positive individual samples and pools (N=50), probably related to the volume of samples used for RNA extraction (200 µL versus 50 µL, respectively). Retrospective testing of positive samples self–collected from October 20th, 2020, using variants–specific amplification kit and spike gene sequencing, found at least 6 residents infected by the B1.1.7 UK variant. Self–collection and pooling approaches allowed large–scale screening for SARS–CoV–2 using less human, material and financial resources. Moreover, this strategy allowed detecting the introduction of SARS–CoV–2 variants in French Polynesia.

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Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs

10.1101/2021.08.14.21262020 ◽

2021 ◽

Author(s):

Irina Kislaya ◽

Eduardo Freire Rodrigues ◽

Vitor Borges ◽

Joao Paulo Gomes ◽

Carlos Sousa ◽

...

Keyword(s):

Viral Load ◽

Conditional Logistic Regression ◽

Secondary Analysis ◽

Vaccination Status ◽

Decision Makers ◽

Control Measures ◽

Rt Pcr ◽

Gene Target ◽

Alpha Variant ◽

Roll Out

Background: The SARS-CoV-2 Delta variant (B.1.617.2), initially identified in India, has become predominant in several countries, including Portugal. Few studies have compared the effectiveness of mRNA vaccines against Delta versus Alpha variant of concern (VOC) and estimated variant-specific viral loads in vaccine infection breakthroughs cases. In the context of Delta dominance, this information is critical to inform decision-makers regarding the planning of restrictions and vaccination roll-out. Methods: We developed a case-case study to compare mRNA vaccines' effectiveness against Delta (B.1.617.2) versus Alpha (B.1.1.7) variants. We used RT-PCR positive cases notified to the National Surveillance System between 17th of May and 4th of July 2021 (week 20 to 26) and information about demographics and vaccination status through the electronic vaccination register. Whole-genome sequencing (WGS) or spike (S) gene target failure (SGTF) data were used to classify SARS-CoV-2 variants. The odds of vaccinated individuals to become infected (odds of vaccine infection breakthrough) in Delta cases compared to Alpha SARS-CoV-2 cases was estimated by conditional logistic regression adjusted for age group, sex, and matched by the week of diagnosis. As a surrogate of viral load, mean RT-PCR Ct values were stratified and compared between vaccine status and VOC. Results: Of the 2 097 SARS-CoV-2 RT-PCR positive cases included in the analysis, 966 (46.1%) were classified with WGS and 1131 (53.9%) with SGTF. Individuals infected with the Delta variant were more frequently vaccinated 162 (12%) than individuals infected with the Alpha variant 38 (5%). We report a statistically significant higher odds of vaccine infection breakthrough for partial (OR=1.70; CI95% 1.18 to 2.47) and complete vaccination (OR=1.96; CI95% 1.22 to 3.14) in the Delta cases when compared to the Alpha cases, suggesting lower mRNA vaccine effectiveness against Delta cases. On our secondary analysis, we observed lower mean Ct values for the Delta VOC cases versus Alpha, regardless the vaccination status. Additionally, the Delta variant cases revealed a Ct-value mean increase of 2.24 (CI95% 0.85 to 3.64) between unvaccinated and fully vaccinated breakthrough cases contrasting with 4.49 (CI95% 2.07 to 6.91) in the Alpha VOC, suggesting a lower impact of vaccine on viral load of Delta cases. Conclusions: We found significantly higher odds of vaccine infection breakthrough in Delta cases when compared to Alpha cases, suggesting lower effectiveness of the mRNA vaccines in preventing infection with the Delta variant. Additionally, the vaccine breakthrough cases are estimated to be of higher mean Ct values, suggesting higher infectiousness with the Delta variant infection. These findings can help decision-makers weigh on the application or lifting of control measures and adjusting vaccine roll-out depending on the predominance of the Delta variant and the coverage of partial and complete mRNA vaccination.

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Self-collection and pooling of samples as resources-saving strategies for RT-PCR-based SARS-CoV-2 surveillance, the example of travelers in French Polynesia

PLoS ONE ◽

10.1371/journal.pone.0256877 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0256877

Author(s):

Maite Aubry ◽

Iotefa Teiti ◽

Anita Teissier ◽

Vaea Richard ◽

Teheipuaura Mariteragi-Helle ◽

...

Keyword(s):

Large Scale ◽

Rna Extraction ◽

French Polynesia ◽

Rt Pcr ◽

Spike Gene ◽

First Case ◽

Main Challenge ◽

Positive Individual ◽

Human Material ◽

Alpha Variant

In French Polynesia, the first case of SARS-CoV-2 infection was detected on March 10th, 2020, in a resident returning from France. Between March 28th and July 14th, international air traffic was interrupted and local transmission of SARS-CoV-2 was brought under control, with only 62 cases recorded. The main challenge for reopening the air border without requiring travelers to quarantine on arrival was to limit the risk of re-introducing SARS-CoV-2. Specific measures were implemented, including the obligation for all travelers to have a negative RT-PCR test for SARS-CoV-2 carried out within 3 days before departure, and to perform another RT-PCR testing 4 days after arrival. Because of limitation in available medical staff, travelers were provided a kit allowing self-collection of oral and nasal swabs. In addition to increase our testing capacity, self-collected samples from up to 10 travelers were pooled before RNA extraction and RT-PCR testing. When a pool tested positive, RNA extraction and RT-PCR were performed on each individual sample. We report here the results of COVID-19 surveillance (COV-CHECK PORINETIA) conducted between July 15th, 2020, and February 15th, 2021, in travelers using self-collection and pooling approaches. We tested 5,982 pools comprising 59,490 individual samples, and detected 273 (0.46%) travelers positive for SARS-CoV-2. A mean difference of 1.17 Ct (CI 95% 0.93–1.41) was found between positive individual samples and pools (N = 50), probably related to the volume of samples used for RNA extraction (200 μL versus 50 μL, respectively). Retrospective testing of positive samples self-collected from October 20th, 2020, using variants-specific amplification kit and spike gene sequencing, found at least 6 residents infected by the Alpha variant. Self-collection and pooling approaches allowed large-scale screening for SARS-CoV-2 using less human, material and financial resources. Moreover, this strategy allowed detecting the introduction of SARS-CoV-2 variants of concern in French Polynesia.

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Assessment of quality of life in patients with the effects of transient ischemic stroke

East European Journal of Neurology ◽

10.33444/2411-5797.2016.6(12).37-39 ◽

2016 ◽

pp. 37-39

Author(s):

A. Babirad

Keyword(s):

Quality Of Life ◽

Ischemic Stroke ◽

Large Scale ◽

Cerebrovascular Diseases ◽

Control Measures ◽

Sociological Research ◽

Cerebrovascular Events ◽

Sf 36 ◽

Angioplasty And Stenting

Cerebrovascular diseases are a problem of the world today, and according to the forecast, the problem of the near future arises. The main risk factors for the development of ischemic disorders of the cerebral circulation include oblique and aging, arterial hypertension, smoking, diabetes mellitus and heart disease. An effective strategy for the prevention of cerebrovascular events is based on the implementation of large-scale risk control measures, including the use of antiagregant and anticoagulant therapy, invasive interventions such as atheromectomy, angioplasty and stenting. In this connection, the efforts of neurologists, cardiologists, angiosurgery, endocrinologists and other specialists are the basis for achieving an acceptable clinical outcome. A review of the SF-36 method for assessing the quality of life in patients with the effects of transient ischemic stroke is presented. The assessment of quality of life is recognized in world medical practice and research, an indicator that is also used to assess the quality of the health system and in general sociological research.

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Investigations, actions and learning from an outbreak of SARS-CoV-2 infection among healthcare workers in the United Kingdom

Journal of Infection Prevention ◽

10.1177/1757177420976798 ◽

2020 ◽

pp. 175717742097679

Author(s):

Kordo Saeed ◽

Emanuela Pelosi ◽

Nitin Mahobia ◽

Nicola White ◽

Christopher Labdon ◽

...

Keyword(s):

Real Time ◽

Healthcare Workers ◽

Healthcare Facility ◽

Rt Pcr ◽

Serum Samples ◽

The United Kingdom ◽

Key Issues ◽

Current Infection ◽

Polymerase Chain ◽

A Current

Background: We report an outbreak of SARS coronavirus-2 (SARS-CoV-2) infection among healthcare workers (HCW) in an NHS elective healthcare facility. Methodology: A narrative chronological account of events after declaring an outbreak of SARS-CoV-2 among HCWs. As part of the investigations, HCWs were offered testing during the outbreak. These were: (1) screening by real-time reverse transcriptase polymerase chain reaction (RT- PCR) to detect a current infection; and (2) serum samples to determine seroprevalence. Results: Over 180 HCWs were tested by real-time RT-PCR for SARS-CoV-2 infection. The rate of infection was 15.2% (23.7% for clinical or directly patient-facing HCWs vs. 4.8% in non-clinical non-patient-facing HCWs). Of the infected HCWs, 57% were asymptomatic. Seroprevalence (SARS-CoV-2 IgG) among HCWs was 13%. It was challenging to establish an exact source for the outbreak. The importance of education, training, social distancing and infection prevention practices were emphasised. Additionally, avoidance of unnecessary transfer of patients and minimising cross-site working for staff and early escalation were highlighted. Establishing mass and regular screening for HCWs are also crucial to enabling the best care for patients while maintaining the wellbeing of staff. Conclusion: To our knowledge, this is the first UK outbreak report among HCWs and we hope to have highlighted some key issues and learnings that can be considered by other NHS staff and HCWs globally when dealing with such a task in future.

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